In the Still of the Night
by Wesfan1234
Summary: John discovers that a boring mission would have been preferable to the hell that he must endure.


Author: WesFan1234

Title: In the Still of the Night

Spoilers: Anything before "Remnants", season five, which this is based upon.

Pairing: John/Elizabeth

Rating: T for some violence and implied torture, character death

Summary: John discovers that a boring mission would have been preferable to the hell that he must endure.

A/N: I haven't posted anything here in so long. I've been on hiatus for a long, long time. So I jumped in and wrote this for LJ's Season 4/Season 5 FixIt Challenge for Stargate: Atlantis. The challenge was to take a prompt and run with it. Mine was something along the lines of "What if it just wasn't Kolya that John encountered" or something like that. I'm a bit rusty right now, but am hoping to get back into the swing of things. Enjoy!

"Don't move."

Oh, his day just kept getting worse and worse. What seemed to be like a normal, run-of-the-mill, boring mission turned into a run for his life.

John raised his arms, hoping he wouldn't pass out from the pain he was in, looking for a way out of this mess. Running wouldn't work because the guy in front of him held a lethal weapon pointed at his head. Maybe if he dove off to the side, he'd be able to roll far enough away. Damn it, and get shot for his efforts.

Crap. See if he ever volunteered to take one beautiful, yet very boring scientist to study plants ever again.

A shot rang out, causing John to jerk in reflex, waiting for the bullet to hit. Why did the guy just shoot him? Wasn't he complying? Ironically enough, the pain he was in wasn't as much as he expected. He had expected to be on the ground. A gut shot would do him in. John looked down to his middle, not seeing any red stains. His head was still intact, his legs functioning. The hand was still missing.

The guy with the gun crumbled before him. Now John dove for cover. Downed trees and slippery, green terrain provided for a bit of a buffer between him and the shooter. His head spun and his whole arm ached as he rolled behind a rather putrid, decaying log that probably had fallen hundreds of years before his birth. The smell almost gagged him as he adjusted his position, trying to figure out who in hell was after him now.

John saw movement off to the right side of the bad guy, who now moaned in agony. Damn. He was hoping that the guy was dead. Served him right for trying to kill him.

Slowly, John inched away from his friendly stinky log, hoping that the shooter didn't spot him slinking off into the forest. As quietly as possible, John crawled his way down (well, it was down, which was why he wanted to jump for it in the first place) to where he had noticed a drop-off. Knowing his luck, it would be a steep drop, followed by a terror-filled moment with no way out.

Keeping his roving eyes battle-ready, John made his descent until he found the edge of what he thought was a small drop. What he hadn't counted on was someone circling around, grabbing his leg and pulling. Why in hell hadn't he thought of that?

His meager luck held as he dropped only five or six feet at most, but the drop was jolting, nonetheless. His teeth cracked together and one of his knees hit a sharp rock. He was momentarily blinded by wet leaves and spikey pine needles in his face. Face down in the muck. It beat a gunshot to the stomach any day.

"Shhh," a soft voice whispered in his ear.

John didn't move a muscle. Whoever had told him to be quiet was now half on top of him, also not moving. Crap and double crap. It was a woman. He could tell by the certain body parts touching him. If it had been Ronon, he'd be home in time for dinner.

John really, really wanted to turn his head, at least to get his nose out of the dank earth. He also wanted to know who his fairy godmother was. It had been too long since a woman had been "this" close to him. Driving that thought from his soil-addled brain, he concentrated on the voices shouting just above them. God, he hoped the people above didn't look in their direction.

"You lose one, then the other," one of the far off voices shouted. Two quick shots, then silence followed. He heard the woman above him choke a little. Turning slightly, he was able to move his head to breathe in fresh air, but not to see the woman's face. Her breath on his neck was harsh, like she had just run a marathon, or heard someone be executed for losing his prisoners.

"Find them," John heard from the executioner. If his other ear hadn't been full of damp earth, he would have sworn on a stack of bibles that the voice was familiar. His arm throbbed just a little bit more from the thought.

"Do not let them get away. We need Atlantis in our hands by tomorrow. Go."

No weapons, no way of contacting Atlantis, no way of reaching the scientists he was guarding, no way of warning everyone that one of his worst nightmares had come true. Kolya had managed to fool them all, yet again, not dying, coming back and in the process chopping his left hand off to gain access to a puddlejumper. The bastard was alive and kicking, had found Atlantis and was planning yet another assault on the city. Double fucking crap.

Before he could turn around and thank his savior for saving his ass, the ground underneath them collapsed, sending them and hundreds of pounds of wet dirt sliding off over that cliff he was worried about. It really did seem like a long way down. He'd been bounced around too much already that day. This time, his head hit first, followed by his shoulder, then the rest of him. The woman promptly added insult to injury by landing directly on top of him. Before blacking out, John this time thanked his lucky stars it wasn't Ronon with him.

* * *

"John, wake up. We have to move. Get up."

"Mom, ten more minutes."

Yeah, he knew he wasn't in his bed back on Earth, all snuggled down under the covers, trying to steal an extra few minutes before school. He was on some godforsaken planet out in the middle of nowhere in a galaxy he sometimes felt he had no reason to be defending in the first place.  
A hand lightly slapped his cheeks, only pissing him off more. He grabbed the offending hand with his good one, reared up and over the person the hand belonged to and pinned her to the ground.

"Listen. I've had about enough shit that I can handle today." John's voice trailed off when he saw who was underneath him.

His day just got worse.

"This is not happening. This is just not fucking happening."

Letting her hand go, John stood up too quickly, swaying as he did so. Not so smart to move quickly after having your head bashed in by a large rock. Maybe he had a concussion and was hallucinating. It happens, he thought. Not to him, but it happens. Maybe he was asleep and dreaming. No, not asleep. His whole body hurt too damn much.

"John, I'm sorry. Are you hurt?"

"Don't talk to me. Don't look at me. You are not real."

Her face looked at him in astonishment and pain. Pain he had caused, more than once.

"What? All I know is I'm here and we need to figure out how to stop Kolya from taking over Atlantis again."

John grabbed her neck with his good hand, pulled her to him roughly, hoping that he would see the real her in those eyes. Shit, he really didn't trust his judgment when it came to Dr. Elizabeth Weir. He needed to trust it now.

"It's me, John. If we don't stop him, Kolya will take what he wants and destroy Atlantis. Let me explain."

He wanted it to be Elizabeth so badly that is stung to have her this close to him. In his dreams, he failed her again and again until he was choking, rolling out of bed and hitting the floor hard. Sometimes he would wake up screaming her name, sometimes he wouldn't even sleep because she would haunt him, taunt him to come save her. He had tried. Oh how he had tried. He had even contemplated disobeying orders, taking a shuttle, and retrieving the "Fran" body. Work always got in the way. Doubt that she was still alive stopped him every time.

"You're not Elizabeth Weir. Don't try to fool me."

Her look of disappointment made his gut tighten up a little.

"You're right. I'm not the Elizabeth Weir you knew. I had to re-engineer another body after the last one was ravaged by space."

John dropped his hand, hoping that she didn't notice his discomfort with her declaration. It was all his fault. He knew what she was going to do when she suggested a particular gate address. No one else was comfortable with her, no one else trusted her while she had inhabited her Fran-lookalike body. He KNEW what she was going to do to save Atlantis, even though she hadn't said much to him before entering that wormhole. That had been Elizabeth in some form or another. Maybe it was the clone, maybe it was the real one who had saved Atlantis. Whoever this was in front of him, he hoped that it was her. But it wasn't.

"No," he declared to her, falling to his one good knee, pain racking the whole side of his body.

She reached for his hair, pulling bits and pieces of leaves and grunt out of it, brushing it off him like she sometimes did when he came back from missions dirty and disgusting. He once saw Lorne smirking as she did this and literally growled back to the Marine.

"Whatever you believe, John, we need to stop him once and for all," Elizabeth told him as she dropped her hands abruptly, probably realizing what she was doing. She often did that too.

"I did stop him, if you don't remember. He's dead. You're dead. Maybe I'm dead too. That would explain some things."

The thought had crossed his mind a few times. His punishment would be to live in purgatory, trying to save Elizabeth from every bad guy they had encountered.

"You're not dead, John. Just a little confused. Kolya found me. He's the reason I'm here."

John shoved her away, scrambling to find a way out of the situation. His good arm gave out as he tried to get up, making him fall hard again to the ground.

"Crap," he groaned as Elizabeth helped him into a sitting position.

"You are in no condition…," Elizabeth tried to explain to him.

Like he ever listened before.

"We should contact Atlantis. Your jumper."

"Is trashed, thanks to Kolya's men. Besides, even if they did 'fix' it like they said they did, Kolya's men probably have it surrounded."

John didn't want to sit there on the damp ground and listen to her any more. He had a job to do. Stop Kolya at all costs. That madman was not going to take out any more of his people. No matter what roadblocks Kolya set up for him, John would conquer them and move on.

Kolya had wondered if John had a deathwish. Elizabeth had expressed that same opinion after one of the more dangerous missions she had sent his team on. He remembered telling her that he was just doing his job, keeping Atlantis safe, for the time being. It had taken him so long to feel comfortable, to feel like he belonged on Atlantis, that he had friends that depended on him and people he could depend upon. So yes, Kolya was sort of right. He had been running away from a sucky life on a planet that threw everything it had at him and spit him out. Atlantis was home. He wasn't going to let a crazy lunatic kill one more person for whom he cared.

"Do we just sit here until they find us again?" Elizabeth inquired while John got his pain under some kind of control.

"You? Yes. Me? I'm not going out without a fight." He definitely didn't want to tell her how many of Kolya's men he had taken out just in case she did work for the bastard.

"If you think for one instant that I'm not going to help you, John Sheppard, you have another thing coming."

Pseudo-Elizabeth looked so fierce standing there, mud caked in her hair, eyes sparking with anger, mostly directed toward him, as usual. The wrath of Elizabeth Weir was well known on Atlantis, with most of it being directed his way while she was commander. God how he missed that.

Elizabeth held out her hand, wanting him to take it in his good one, to trust her enough to let her help. If she was the enemy, he'd find out too late to fix it. If she wasn't, he definitely would need the help.

* * *

Setting the next trap was much easier with another set of hands. There were only so many tasks he could perform with just one hand. When they had taken down three more Genii, John suggested they slowly make their way back to the jumper. He'd get a better idea how many more troops Kolya had brought with him.

"How did Kolya find you?" John whispered as they made their way through the dense forest.

"By accident. A race called the Sacari found me drifting, helped me with building a new body, and then let me live amongst them. A human living with an alien race attracted attention unfortunately. The Genii attacked the Sacari, who had no weapons to defend themselves."

John figured that someone probably got hurt in that exchange. Her grief-stricken face told him that it hadn't gone easy.

"Listen. I understand that you may have gone through a difficult time."

Elizabeth stopped walking, eyes wide and full of anger for him. "You still don't believe me. It's me, John. What do I have to do to make you believe that I am who I am? The Sacari risked their lives to try and save me. I owe them so much."

"Save it," he growled back. "You ended up leading Kolya right to Atlantis."

A noise distracted John from their argument. Pulling Elizabeth down beside him, they watched as one of Kolya's men slowly made his way through the brush, encountering the trap that was just set. The man sprung into the air, caught by his foot, swinging madly as his gun fell to the ground. John grabbed it, whacked the guy on the head and ran just in case there was another one close by.

So it went on for a few hours; men either trapped or dead from John's handiwork. He and Elizabeth didn't speak much in those few hours. They always had worked well as a team. He had missed that part the most. Sam Carter and Richard Woolsey were adequate as commanders of Atlantis. But they never just knew what he was thinking. The mental connection between himself and Elizabeth was sometimes joked about throughout Atlantis, especially by the Marines. They were right. Not that he and Elizabeth agreed on everything. Everyone knew when they disagreed too.

"I'm sorry," Elizabeth whispered as they moved through a particularly dense part of the forest.

Water from the leaves dripped down on their heads, making John shiver just a little. It was possible he was developing an infection from all the injuries he had sustained. His whole arm was now numb. The blood loss hadn't weakened him, yet.

"If I could prove to you who I am, would that make a difference?" Elizabeth asked as she reached out her hand to stop him.

Would it matter if she was alive? Hell, yes. He had given up hope so long ago.

"It doesn't matter," he responded, but didn't really mean.

"It does, to me. Let me look at your arm."

Elizabeth bandaged his wound tighter, making him grimace at the pain she was causing. Having her that close to him gave him an opportunity to study her. Even dirty, she smelled like Elizabeth. With his thumb, he tried to wipe a little dirt off of her pale cheek, making the smudge worse. Her eyes caught his, looking a bit startled at his gesture. They were mere inches from one another.

That damn ESP thing that they had was working full tilt at that moment. John wanted nothing more than to pull her to him and not let go. Elizabeth had to go and ruin his thought process by moving closer. The few hugs and one memorable kiss that they shared had nothing on what was going on between them at the moment. John's brain went haywire as he really looked at this Elizabeth. If it wasn't the real Elizabeth, it certainly was the best copy he'd met.

Personal space was never an issue with the two of them. A brush of the hands, standing right next to each other, sitting with their bodies mere inches away from each other; there was definitely no problems with personal space issues at all. As he stood there not an inch from Elizabeth, he couldn't move any further.

Why was it that every damn time they touched, Elizabeth had to be the one to make the first move? Every hug, that kiss, every damn time, she was the one to break the ice and just do it. This time was no exception. He didn't even want to close his eyes as he watched her gently touch her lips to his.

His brain told him to end it, but everything else told him that this was right. As he pulled her deeper into the kiss, he closed his eyes, savoring this one moment just like he did the last time this had happened. Even taken over by an alien entity hadn't dampened his awareness of her lips on his. Why he hadn't done this again while she was on Atlantis was really stupid on his part.

Elizabeth jerked a split second after John heard the loud bang just off to his side. Instinct kicked in as he dove for cover, shielding Elizabeth from more gunfire. He felt the blood on her back, his good hand covered in it. Looking at her face for any sign of life, he watched as she took her last breath and was still.

He had dreamed of this day constantly, even after she was gone from his life. In the back of his mind, he knew she might be out there somewhere in the universe. Now, she wouldn't be. Standing up, he fired at the perpetrator, realizing that it was indeed Kolya who had ruined his life once again by shooting the one person he cared about most.

* * *

They played a cat and mouse game until finally encountering each other near a cliff once again. John was weakening from his injuries and the hurt of losing Elizabeth once again. He really didn't care if he died as he careened over the side of that cliff and grabbed onto a root. Falling to his death wouldn't hurt as much as watching her die in his arms.

Then Kolya told him to use his missing hand. The brain can still play tricks on you, but as he pulled it out of his jacket, it was whole once again. It really was all a dream, an elaborate scheme to keep John busy, Kolya or whoever that was told him. The image of Kolya had been sent to distract him, keep him off balance until the Sacari could convince Rodney and Woolsey to send them on their merry way. It was all in John's mind. He had tortured himself with Kolya's image and Elizabeth's kiss, losing his hand and finally losing the one thing that he had ever truly cared about in his life. His darkest fears were exposed by some alien just trying to find a home.

He turned when he heard Elizabeth's voice once again.

"We didn't want to deceive you, John. These people have a chance of starting over, establishing a new life on a planet that can sustain them."

The words rang hollow as John walked away. It had all been so real.

Arriving back on Atlantis, John hid in his room while Rodney and the others prepared the alien device to be sent to a suitable planet. He filed his mission report, but left out the part where Elizabeth had played a role in his mind's deception. It was bad enough that he had to tell everyone that Kolya had been sent to distract him. Keller would be recommending that he talk to the shrink instead of just letting him hide out in his room.

Just when he thought it would be safe to roam the halls once again, Rodney caught up with him, asking him if he wanted to help with transporting the Sacari device. John jumped at the chance to put all this behind him, wheeling the device to the gateroom. As he half listened to Woolsey talk to the alien artificial intelligence, John wondered why the Sacari would think he was such a threat to them.

John felt a hand on his shoulder, thinking it was Rodney trying to get him to move forward with the device. He would be glad to get rid of the thing so Atlantis could return to normal once again.

As he turned to look at Rodney, he saw Elizabeth instead. Woolsey's eyebrows shot up and Rodney's mouth formed an "oh", but no sound came out. Their reactions probably meant that both men could see her.

"Thank you all, for giving the Sacari another chance," Elizabeth announced as she nodded toward the AI.

"Sheppard, want to tell us what in hell is going on?" Rodney asked as he passed the alien device to the AI.

"You're real," John directed Elizabeth's way.

"As real as I can be. I must be going."

She didn't want to go. That ESP thing worked when he didn't want it to work. Elizabeth had to go. She didn't have a choice in the matter.

"Why?" was all John could get out.

"I knew that you would help the Sacari."

"You can't leave," Rodney added in as Elizabeth backed away to join the AI.

"I don't have a choice, Rodney."

"Dr. Weir. Maybe there is something we can do to facilitate your staying, even just a bit longer," Woolsey interjected.

John got it now. Everything. Damn glowly people. A smile formed on his face as he watched in awe as Elizabeth started to glow. That damn glow was the best thing he'd seen in a long time.  
"She ascended," Rodney said, stating the obvious.

The whole control room lit up with the ascended Elizabeth's aura. Something somehow passed through John, making him feel lighter, more settled than he had felt in ages. He swore he actually felt Elizabeth's hand touch his face right before she swooped away. He even thought she told him thank you too, but maybe that was just him imagining things.

The whole control room was eerily silent for what seemed like ages until Woolsey gave the command for the device to be transported. After Rodney and Woolsey walked away, with the former chatting nonstop about what had just happened, John stood there at attention, very much like he did the last time Elizabeth had disappeared through the wormhole, never to return.

This time it was more of a happy ending of sorts. One had to want to ascend. The sacrifice that Elizabeth had made stopping the Replicators had been necessary. Could that one last sacrifice, going through that wormhole, been the deciding factor for her to escape her fate of floating in space?

As he shared a cigar with Woolsey, which was a toast to a job well done, John Sheppard felt at peace for once in his life. He missed Elizabeth more than he imagined he could, but she had chosen to do good, to help beings in need. It was probably more than he could ever do in his lifetime. John knew that Elizabeth Weir was an extraordinary woman, his feelings for her aside. He wouldn't be worried now that she was lost. Elizabeth had finally found her calling, he thought to himself as he watched the sun set on the horizon.


End file.
